Atheist sues to have his child removed from Catholic school

A Catholic mother wants to send her son to Catholic school but the atheist father wants to send the son to public school because he doesn't want his child indoctrinated:

According to Kagin, when Ryan and his wife got divorced, a judge ordered their son continue attending a Catholic school.

[...]

Kagin said part of Kentucky’s constitution reads, "Nor shall any man be compelled to send his child to any school to which he may be conscientiously opposed."

Kagin said going by the law, the judge's decision should be easy, but he doesn't know how much the judge will consider Ryan’s son's wishes on the matter.

OK, so let me get this straight, if the father doesn't want the child sent to Catholic school, then the state should force the child to go to public school even though the mother wants him to go to Catholic school (and possibly the son wants to go). What is this? The constitution only protects the father's rights? Not the mother's rights? What about the part that says "or prohibiting the free exercise thereof?" The state doesn't have the right to stop her from sending her child to Catholic school. I think this case is in constitutional limbo :-)

BTW, the Friendly Atheist states that if the law is followed, this should be an open and shut case. Do atheists really believe that the father's rights supersede that of the child and the mother? Or is that only in the case where the mother is a Catholic and the father is an atheist?